Download or read book Structural and Biochemical Studies of Replicative Helicase Loading in Bacteria written by Iris Vanessa Hood and published by . This book was released on 2015 with total page 172 pages. Available in PDF, EPUB and Kindle. Book excerpt: The initiation of DNA replication represents a defining commitment to the proliferation of all cellular organisms. Dedicated ATP-dependent initiation factors specifically mark replication start sites or "replication origins" and, together with ATP-dependent helicase loaders, help coordinate productive assembly of the replisome. In many bacterial species, helicase loaders belonging to the DnaC/I family of proteins assist the bacterial initiator factor DnaA with loading and activation of DnaB-type replicative helicases. Despite advances in understanding some of the essential proteins and common principles underlying initiation strategies, major questions still persist in defining how initiation programs are executed at the molecular level. The present dissertation presents a combination of structural and biochemical studies of the DnaC helicase loader and DnaA initiator from the Gram-negative bacterium Escherichia coli (E. coli) and the DnaI helicase loader from the Gram-positive bacterium Staphylococcus aureus (S. aureus). For the E. coli work, I developed several fluorescence-based helicase assays to help define the particular contributions of both DnaA and DnaC in promoting loading of DnaB at a replication origin. Investigations of DnaA mutants in this helicase assay revealed the importance of the initiator's N-terminal helicase binding domain in recruiting DnaB to a nascent bubble or fork to facilitate helicase loading. Parallel studies of the E. coli DnaC demonstrated: (i) that the loader's N-terminal DnaB binding domain is sufficient for activation of E. coli DnaB's duplex DNA unwinding activity and (ii) that the AAA+-family ATP binding and hydrolysis domain of DnaC likely serves as a regulatory element that helps enhance the efficiency of helicase activation. To better characterize the activity of a Gram-positive S. aureus DnaI helicase loader, I structurally and biochemically characterized the protein's ATPase domain and activity, and also investigated how a particular viral peptide inhibitor from phage 77, termed "ORF104", interferes with host DNA replication by blocking SaDnaI activity. Comparative structural analyses, combined with biochemical studies of SaDnaI revealed not only how the viral inhibitor 77ORF104 blocks loader function but also revealed insights into how bacterial helicase loaders may in general auto-regulate their function. A complimentary viral-host interaction study of another staph-specific viral peptide that also inhibits host DNA replication ("ORF078" from phage 71) has revealed another promising anti-bacterial strategy: preliminary binding studies indicate that this gene product binds primase through its helicase-binding domain. Overall, the studies presented in this dissertation provide multiple new insights into fundamental mechanisms underlying the initiation of DNA replication. One is an enhanced understanding of the role that the E. coli DnaA initiator and DnaC loader serve in recruiting the DnaB helicase to a replication origin. The other describes a novel viral mechanism for inhibition of the S. aureus DnaI helicase loader that helps establish how a virus may exploit an existing auto-regulatory element of the bacterial helicase loader as part of a strategy to inhibit host DNA replication. These findings collectively not only answer long-standing questions in the field, but also open up new avenues for future inquiry.
Download or read book Structural and Biochemical Studies of Bacterial DNA Replication Initiation written by Melissa Mott (Lynn) and published by . This book was released on 2009 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural and Biochemical Mechanisms of Replicative Helicase Loading in E Coli written by Sarah Diane McMillan and published by . This book was released on 2024 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: DNA replication is an essential process in all organisms and begins with loading of the replicative helicase, DnaB. This process requires a loading factor, DnaC, which helps to crack open the hexameric helicase to facilitate loading onto DNA. At the origin of replication, an initiator protein recruits the DnaB/DnaC complex to initiate replication in a sequence-dependent manner. However, once replication is initiated, the replication machinery (replisome) can encounter barriers that lead to the replisome dissociating from DNA. When this happens, the DnaB/DnaC complex must be recruited back to the DNA in a structure specific manner with the help of Replication Restart Proteins (RRPs). In this thesis, I characterize the DnaB loading process and examine how a RRP, PriC, mechanistically loads the DnaB/DnaC complex. First, in Chapter 2, I characterize a panel of DnaC variants that alter the type of substrate that DnaB is loaded onto. This work has increased our understanding of how replicative helicase loading is regulated. I next characterize PriC-mediated DnaB loading through a cryo-EM structure that shows that PriC binds to the DnaB/DnaC complex in the "crack" that is exposed when DnaC binds to the helicase (Chapter 3). Finally, I characterize a panel of RRP variants that decrease loading of DnaB by disrupting a protein-protein interface between two RRPs (Chapter 4). Overall, my results increase our understand of DnaB loading, both generally and in the context of replication restart.
Download or read book Molecular Biology of the Cell written by and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Structural and Biochemical Studies of Origin Opening by Bacterial Replication Initiators written by Karl Edward Duderstadt and published by . This book was released on 2011 with total page 262 pages. Available in PDF, EPUB and Kindle. Book excerpt: All organisms depend on a variety of oligomeric ATPase assemblies to carry out essential cellular processes ranging from proteolysis and membrane trafficking to signaling events and nucleic acid transactions. The onset of DNA replication is one such process, relying on dedicated, ATP-dependent initiation factors to coordinate origin recognition and replisome assembly. Although cellular initiators and the initiators of certain classes of double-stranded DNA viruses use a variety of different strategies to process replication origins, they all possess a common adenine nucleotide-binding fold belonging to the AAA+ family of ATPases. To better understand the origin processing mechanism of AAA+ initiators, I performed a series of biochemical and structural studies with the bacterial initiator DnaA. In one study, I used structure-guided mutagenesis, biochemical, and genetic approaches to show that different oligomeric conformations of DnaA play distinct roles in controlling the progression of initiation. In a second study, I showed both crystallographically and in solution that the AAA+ domains of a spiral DnaA oligomer bind and extend single-stranded DNA segments in a RecA-like manner. These structural insights, combined with a novel DNA melting assay, indicate that DnaA uses its AAA+ domain to directly open replication origins by an active, ATP-dependent stretching mechanism. The studies presented in this dissertation provide a new model for origin opening in bacteria that has implications for the origin processing mechanism of all initiators.
Download or read book Molecular Biology written by Nancy Craig and published by Oxford University Press. This book was released on 2014-05 with total page 945 pages. Available in PDF, EPUB and Kindle. Book excerpt: The biological world operates on a multitude of scales - from molecules to tissues to organisms to ecosystems. Throughout these myriad levels runs a common thread: the communication and onward passage of information, from cell to cell, from organism to organism and ultimately, from generation to generation. But how does this information come alive to govern the processes that constitute life? The answer lies in the molecular components that cooperate through a series of carefully-regulated processes to bring the information in our genome to life. These components and processes lie at the heart of one of the most fascinating subjects to engage the minds of scientists today: molecular biology. Molecular Biology: Principles of Genome Function, Second Edition, offers a fresh approach to the teaching of molecular biology by focusing on the commonalities that exist between the three kingdoms of life, and discussing the differences between the three kingdoms to offer instructive insights into molecular processes and components. This gives students an accurate depiction of our current understanding of the conserved nature of molecular biology, and the differences that underpin biological diversity. Additionally, an integrated approach demonstrates how certain molecular phenomena have diverse impacts on genome function by presenting them as themes that recur throughout the book, rather than as artificially separated topics As an experimental science, molecular biology requires an appreciation for the approaches taken to yield the information from which concepts and principles are deduced. Experimental Approach panels throughout the text describe research that has been particularly valuable in elucidating difference aspects of molecular biology. Each panel is carefully cross-referenced to the discussion of key molecular biology tools and techniques, which are presented in a dedicated chapter at the end of the book. Molecular Biology further enriches the learning experience with full-color artwork, end-of-chapter questions and summaries, suggested further readings grouped by topic, and an extensive glossary of key terms. Features: A focus on the underlying principles of molecular biology equips students with a robust conceptual framework on which to build their knowledge An emphasis on their commonalities reflects the processes and components that exist between bacteria, archae, and eukaryotes Experimental Approach panels demonstrate the importance of experimental evidence by describing research that has been particularly valuable in the field
Download or read book Molecular Life Sciences written by Robert D. Wells and published by Springer. This book was released on 2018-01-12 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Life Sciences: An Encyclopedic Reference will focus on understanding biological phenomena at the level of molecules and their interactions that govern life processes. The work will include articles on genes and genomes, protein structure and function, systems biology using genomics and proteomics as the focus, molecular aspects of cell structure and function, unifying concepts and theories from biology, chemistry, mathematics and physics that are essential for understanding the molecular life sciences (including teaching perspectives and assessment tools), and basic aspects of the various experimental approaches that are used in the Molecular Life Sciences.
Download or read book DNA Helicases and DNA Motor Proteins written by Maria Spies and published by Springer Science & Business Media. This book was released on 2012-11-19 with total page 308 pages. Available in PDF, EPUB and Kindle. Book excerpt: In recent years, a number of groundbreaking structural and mechanistic studies deepened our understanding of helicase mechanisms and established new approaches for their analyses. Many fundamental mechanistic questions ranging from the mechanism of force generation, mechanochemical coupling to distinct mechanisms by which the same enzyme translocates on DNA removing obstacles, unwinds DNA and/or remodels nucleoprotein complexes, however, remain to be answered. It is even less understood how the helicase motors are incorporated into a wide range of genome maintenance and repair machines. The field has reached a stage when the studies of molecular mechanisms and basic biology of helicases can and shall be integrated with the studies of development, cancer and longevity. The objective of this book is to provide the first systematic overview of structure, function and regulation of DNA helicases and related molecular motors. By integrating the knowledge obtained through the diverse technical approaches ranging from single-molecule biophysics to cellular and molecular biological studies the editors aim to provide a unified view on how helicases function in the cell, are regulated in response to different cellular stresses and are integrated into large macromolecular assemblies to form a complex and adaptive living system.
Download or read book The Bacterial Cell Coupling between Growth Nucleoid Replication Cell Division and Shape written by Arieh Zaritsky and published by Frontiers Media SA. This book was released on 2016-05-02 with total page 326 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial Physiology was inaugurated as a discipline by the seminal research of Maaløe, Schaechter and Kjeldgaard published in 1958. Their work clarified the relationship between cell composition and growth rate and led to unravel the temporal coupling between chromosome replication and the subsequent cell division by Helmstetter et al. a decade later. Now, after half a century this field has become a major research direction that attracts interest of many scientists from different disciplines. The outstanding question how the most basic cellular processes - mass growth, chromosome replication and cell division - are inter-coordinated in both space and time is still unresolved at the molecular level. Several particularly pertinent questions that are intensively studied follow: (a) what is the primary signal to place the Z-ring precisely between the two replicating and segregating nucleoids? (b) Is this coupling related to the structure and position of the nucleoid itself? (c) How does a bacterium determine and maintain its shape and dimensions? Possible answers include gene expression-based mechanisms, self-organization of protein assemblies and physical principles such as micro-phase separations by excluded volume interactions, diffusion ratchets and membrane stress or curvature. The relationships between biochemical reactions and physical forces are yet to be conceived and discovered. This e-book discusses the above mentioned and related questions. The book also serves as an important depository for state-of-the-art technologies, methods, theoretical simulations and innovative ideas and hypotheses for future testing. Integrating the information gained from various angles will likely help decipher how a relatively simple cell such as a bacterium incorporates its multitude of pathways and processes into a highly efficient self-organized system. The knowledge may be helpful in the ambition to artificially reconstruct a simple living system and to develop new antibacterial drugs.
Download or read book Clinical Molecular Diagnostics written by Shiyang Pan and published by Springer Nature. This book was released on 2021-07-08 with total page 889 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book covers the discovery of molecular biomarkers, the development of laboratory testing techniques and their clinical applications, focusing on basic research to clinical practice. It introduces new and crucial knowledge and ethics of clinical molecular diagnosis. This book emphasizes the applications of clinical molecular diagnostic test on health management, especially from different diseased organs. It lets readers to understand and realize precision healthcare.
Download or read book Helicases from All Domains of Life written by Renu Tuteja and published by Academic Press. This book was released on 2018-10-15 with total page 200 pages. Available in PDF, EPUB and Kindle. Book excerpt: Helicases are ubiquitous enzymes found throughout evolution. Research in the helicase field has been going on for a long time now but in recent past with the completion of so many genomes, these enzymes have been discovered in a number of organisms. But the available literature is scattered. The huge number of identified DNA and RNA helicases, along with the structural and functional differences among them, make difficult for the interested scholar to grasp a comprehensive view of the field. Helicases from all Domains of Life is the first book to compile information about helicases from many different organisms in one place. Knowledge of the functions and features of helicases across the different kingdoms of life are a valuable source of novel ideas and information The book begins with a chapter on the evolutionary history of helicases followed by three "overview" chapters: one for bacteria/archaea (which are not mentioned), one for plants/algae and one for human helicases The overview chapters are followed by specific chapters on selected helicases of great importance from a biological/applicative point of view
Download or read book Prokaryotic Metabolism and Physiology written by Byung Hong Kim and published by Cambridge University Press. This book was released on 2019-05-16 with total page 509 pages. Available in PDF, EPUB and Kindle. Book excerpt: Extensive and up-to-date review of key metabolic processes in bacteria and archaea and how metabolism is regulated under various conditions.
Download or read book Physical Biology of the Cell written by Rob Phillips and published by Garland Science. This book was released on 2012-10-29 with total page 1089 pages. Available in PDF, EPUB and Kindle. Book excerpt: Physical Biology of the Cell is a textbook for a first course in physical biology or biophysics for undergraduate or graduate students. It maps the huge and complex landscape of cell and molecular biology from the distinct perspective of physical biology. As a key organizing principle, the proximity of topics is based on the physical concepts that
Download or read book Crystal Structure and Biochemical Analysis of an E1 E2 Complex of the Human Papillomavirus Type 18 written by Eric Anthony Abbate and published by . This book was released on 2003 with total page 316 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Download or read book Encyclopedia of Biological Chemistry written by and published by Academic Press. This book was released on 2013-01-08 with total page 3223 pages. Available in PDF, EPUB and Kindle. Book excerpt: The 4-volume Encyclopedia of Biological Chemistry, Second Edition, represents the current state of a dynamic and crucial field of study. The Encyclopedia pulls together over 500 articles that help define and explore contemporary biochemistry, with content experts carefully chosen by the Editorial Board to assure both breadth and depth in its coverage. Editors-In-Chief William J. Lennarz and M. Daniel Lane have crafted a work that proceeds from the acknowledgement that understanding every living process-from physiology, to immunology, and genetics-is impossible without a grasp on the basic chemistry that provides its underpinning. Each article in the work provides an up-to-date snapshot of a given topic, written by experts, as well as suggestions for further readings for students and researcher wishing to go into greater depth. Available on-line via SciVerse ScienceDirect, the functionality of the Encyclopedia will provide easy linking to referenced articles, electronic searching, as well an online index and glossary to aid comprehension and searchability. This 4-volume set, thoroughly up-to-date and comprehensive, expertly captures this fast-moving field Curated by two esteemed editors-in-chief and an illustrious team of editors and contributors, representing the state of the field Suggestions for further readings offer researchers and students avenues for deeper exploration; a wide-ranging glossary aids comprehension
Download or read book Flexible Viruses written by Vladimir Uversky and published by John Wiley & Sons. This book was released on 2012-02-07 with total page 532 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book provides up-to-date information on experimental and computational characterization of the structural and functional properties of viral proteins, which are widely involved in regulatory and signaling processes. With chapters by leading research groups, it features current information on the structural and functional roles of intrinsic disorders in viral proteomes. It systematically addresses the measles, HIV, influenza, potato virus, forest virus, bovine virus, hepatitis, and rotavirus as well as viral genomics. After analyzing the unique features of each class of viral proteins, future directions for research and disease management are presented.
Download or read book Bacillus Subtilis and Its Closest Relatives written by A. L. Sonenshein and published by . This book was released on 2002 with total page 664 pages. Available in PDF, EPUB and Kindle. Book excerpt: Focusing on issues of gene organization, regulation, and evolution in the context of the whole life of the cell, this new volume complements the editors' classic 1993 volume Bacillus subtilis and Other Gram-Positive Bacteria. Building upon the previous edition, Bacillus subtilis and Its Closest Relatives contains an updated annotation of the complete B. subtilis genome and includes a unique compilation of major pathways of metabolism and macromolecular synthesis, correlating genes and proteins and assigning new functions to many genes. It also provides clear explanations of the major regulatory mechanisms that are unique to gram-positive bacteria as well as an overview of their special properties. This essential reference offers detailed, current information and is valuable reading for microbiologists, biotechnologists, and students.
